Acidobacteria Actinobacteria Alphaproteobacteria
Aquificae Bacteroidetes/Chlorobi Betaproteobacteria
Chlamydiae/Verrucomicrobia Chloroflexi Cyanobacteria
Deinococcus-Thermus Deltaproteobacteria Epsilonproteobacteria
Firmicutes Fusobacteria Gammaproteobacteria
Other Bacteria Planctomycetes Spirochaetes
Thermotogae
Classification of phyla is from NCBI page
Search:
106 projects found  

4 accessions found for Mycobacterium gilvum PYR-GCK  

Data for CP000656  

Available Atlases
Other Plots
hmmsearch - search a sequence database with a profile HMM
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: /home/projects/MicrobialGenomicsGroup/Packages/hmmdata-1.0.0.package/Resources/noarch/TCS/HisKA_3.hmm [HisKA_3]
Sequence database: CP000656.Gprot.fsa
per-sequence score cutoff: >= 30.1 [TC1]
per-domain score cutoff: >= 30.1 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA_3
Accession: PF07730.2
Description: Histidine kinase
[HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
CP000656_2263 CDS_2371855-2370518 75.8 6.3e-22 1
CP000656_4985 CDS_5340273-5341472 64.3 1.5e-18 1
CP000656_3820 CDS_4107807-4106080 44.0 1.5e-12 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000656_2263 1/1 244 311 .. 1 70 [] 75.8 6.3e-22
CP000656_4985 1/1 196 265 .. 1 70 [] 64.3 1.5e-18
CP000656_3820 1/1 385 450 .. 1 70 [] 44.0 1.5e-12

Alignments of top-scoring domains:
CP000656_2263: domain 1 of 1, from 244 to 311: score 75.8, E = 6.3e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RI R+LHDsv +L ++++ ++la++ l d+dp+ ar+ ++e+
CP000656_2 244 ERHRIERDLHDSVQPRLVSLAMTIGLAQTKL--DSDPPTARALIAEA 288

relarealaevRrllgdLRpaal<-*
++ a+ al e+R++++++ p++l
CP000656_2 289 HDEAKNALVELRNVVRGIAPTIL 311

CP000656_4985: domain 1 of 1, from 196 to 265: score 64.3, E = 1.5e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER+R+A ++HD+++Q+L ++ l++a++++ ++++++ ++ e+ld
CP000656_4 196 ERRRLAGDIHDGISQRLVTLSYRLDAAAQAA--KSPADhaALTEQLD 240

eirelarealaevRrllgdLRpaal<-*
++rela+ +l+e+R+++++LRp++l
CP000656_4 241 RARELADLTLQEARAAISGLRPPVL 265

CP000656_3820: domain 1 of 1, from 385 to 450: score 44.0, E = 1.5e-12
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R RIAR+LHD v Q+L+a+ l l++ +++ +++ e++++l +
CP000656_3 385 DRDRIARDLHDHVIQRLFAVGLSLQGSIARA--RSE--EVQQRLSAN 427

relarealaevRrllgdLRpaal<-*
+ ++ ++e+R ++ dL+ +
CP000656_3 428 VDDLQSVIQEIRTAIFDLHGGSS 450


Histogram of all scores:
score obs exp (one = represents 16 sequences)
----- --- ---
-14 4 0|=
-13 35 0|===
-12 96 58|===*==
-11 160 480|========== *
-10 521 1114|================================= *
-9 893 1265|======================================================== *
-8 804 975|=================================================== *
-7 752 613|======================================*========
-6 611 347|=====================*=================
-5 600 186|===========*==========================
-4 296 97|======*============
-3 178 49|===*========
-2 124 25|=*======
-1 66 13|*====
0 34 6|*==
1 21 3|*=
2 14 1|*
3 12 0|=
4 3 0|=
5 1 0|=
6 3 0|=
7 5 0|=
> 8 8 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3289.4475
P(chi-square) = 0

Total sequences searched: 5241

Whole sequence top hits:
tophits_s report:
Total hits: 3
Satisfying E cutoff: 3
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 3
Satisfying E cutoff: 3
Total memory: 21K


Acknowledgements:

This research is funded by:

Developed by: